Peptide predictor

Video Demo: https://youtu.be/e5vSPkWIlJ0?si=TkNYAqvFqJXmPGhB

That is a script to predict peptides obtained after an action of different proteinases. This software was heavily inspired by PeptideCutter tool from Expasy (https://web.expasy.org/peptide_cutter/).

Input/output

The script can accept FASTA files with one or multiple records as an input. The output of the script is PDF file with the results of protein digestion. Each file is autonamed according to this pattern: "<Enzyme_chosen>peptides<Digestion_mode>from<Protein_description_from_FASTA_header>". That means that user can easily distinguish the different files just by reading the name of the file. It already contains the nme of the enzyme which digests the target protein, digestion mode, and protein description from FASTA header. Each file is in separate folder: "<Enzyme_chosen>peptides<Digestion_mode>from<Protein_description_from_FASTA_header>datetime". All result folders are in folder "results", which creates during the first run of the program.

Enzymes available:

1. Arg-C_proteinase
2. Asp-N_endopeptidase
3. Chymotrypsin_high_specificity
4. Chymotrypsin_low_specificity
5. Trypsin
6. Papain
7. Pepsin_pH1.3
8. Pepsin_pH_2

Example of usage

The script provides 3 modes to digest a protein: single digestion, parallel digestion and sequential digestion. All modes need user to input the name of FASTA file ("filename.fasta"), choose the number wich represents the digestion mode and enter the number which represents the enzyme/enzymes wanted. User can input via CLI or via interactive prompt. Interactive propmpt is recommended for a first-time use to familiarize with workflow of the program. CLI input also allows for multiple files to analyse without the need for specific Bash script. Example of multifile CLI input:

python project.py --input_files file1.fasta file2.fasta --digestion_mode 1 --input_enzyme_number 5

Single digestion

Single digestion mode cleaves protein with only one user-selected enzyme. The outfile contains the number of peptides obtained, the quantity of cleavage sites, the list of an actual peptides, the cleavages sites list and the site-peptide relationship. Example:

python project.py --input_files sequence.fasta --digestion_mode 1 --input_enzyme_number 5

--- Processing File: sequence.fasta ---
     ✓ Look for results in: results/
        └── Trypsin_Single_conglutin_beta_Lupinus_angustifolius_2026_01_13-20_10/
            └── Trypsin_peptides_Single_digest_from_conglutin_beta_Lupinus_angustifolius.pdf

[1/1] Processed accession number: ABR21772.1

Parallel digestion

Parallel digestion mode cleaves protein with 2 or more user-selected enzymes and writes results in order of selection. It allows to compare the results of digestion by different enzymes. The outfile contains the number of peptides obtained, the quantity of cleavage sites, the list of an actual peptides, the cleavages sites list and the site-peptide relationship for both enzymes selected. First page of resulting PDF contains the clickable table of contents to allow user easily orient between pages. Example:

python project.py --input_files sequence.fasta --digestion_mode 2 --input_enzyme_number 5,1

--- Processing File: sequence.fasta ---
     ✓ Look for results in: results/
        └── Trypsin_Arg-C_proteinase_Parallel_conglutin_beta_Lupinus_angustifolius_2026_01_13-20_12/
            └── Trypsin_Arg-C_proteinase_peptides_Parallel_digest_from_conglutin_beta_Lupinus_angustifolius.pdf

[1/1] Processed accession number: ABR21772.1

Sequential digestion

Sequential digestion cleaves protein with 2 or more user-selected enzymes one by one: the peptides from first enzymes are substrate for a second one and so on. The outfile contains the number of peptides obtained, the quantity of cleavage sites, the list of an actual peptides, the cleavages sites list and the site-peptide relationship for first enzyme. For every next enzyme file contains the name of corresponding enzyme, the number of peptides produced in this step of digestion, the list of peptides obtained and per-peptide breakdown: original peptide, produced peptide, the number of cleavage site from the original peptide. If secondary digestion did in fact occur then the produced peptide is blue and cleavage sites are red. First page of resulting PDF contains the enzyme-selected, number of digestions and clickable table of contents to allow user easily orient between pages. Example:

python project.py --input_files sequence.fasta --digestion_mode 3 --input_enzyme_number 5,1```

--- Processing File: sequence.fasta ---
     ✓ Look for results in: results/
        └── Trypsin_Arg-C_proteinase_Sequential_conglutin_beta_Lupinus_angustifolius_2026_01_13-20_14/
            └── Trypsin_Arg-C_proteinase_peptides_Sequential_digest_from_conglutin_beta_Lupinus_angustifolius.pdf

[1/1] Processed accession number: ABR21772.1

All snippet commands and results are written for the test file sequence.fasta. You can use it to test the script. There is also a result file example to look: Trypsin_ArgC_proteinase_peptides_Sequential_digest_from_conglutin_beta_Lupinus_angustifolius.pdf

Requirements:

Python 3.10.12 (no tests conducted to assure compatibility with previous or next versions)
biopython==1.86
fpdf2==2.8.5
pytest==9.0.2